Presented in five easy reasons.
1. The Orcs don't like him.
True, Thrall was a visionary. True, Thrall freed his people from their bloodlust. True, Thrall led his people to safety.
But at the same time, Thrall led them to a desert and left them to starve while he went off to play hero. He routinely turned his back on the Horde to increase his own glory and rarely seemed to care about them beyond the ideals he hoped they would portray one day.
Garrosh is portrayed as being adored by nearly the entirety of the Orcish population because, unlike Thrall, he actually gave a damn about what happened to his people. He's a supremacist, sure, but he's not a glory-seeking traitor like Thrall.
2. The Alliance doesn't like him.
Thrall is basically responsible for every murder Garrosh has ever committed. He saw the kind of monster Garrosh would become in Northrend and decided to turn over to him the whole strength of the Horde's military might while he went off to go play in the Maelstrom for awhile.
When Garrosh murdered the elves, Thrall did nothing. When Garrosh murdered Cairne, Thrall did nothing. When Garrosh murdered every man, woman and child in Theramore, Thrall did nothing. And Thrall was the only one who could do something.
Thrall is the number one enemy of the Alliance.
3. He doesn't make sense.
Here's where the big story problems with Thrall emerge.
So, at the end of 5.1, Thrall is given news of the assassination attempt on Vol'jin. This, it seems, is enough to stir him to finally stand up to Garrosh.
What makes that the straw that broke the camel's back? Thrall clearly doesn't take Vol'jin all that seriously, since he ignored Vol'jin's warnings about Garrosh in the first place. So why does he care about Vol'jin now?
Some people say that he couldn't respond to Theramore because he was off being the World-Shaman. In the books, it's said that Garrosh was summoning Molten Giants from the Firelands and Krakens from Vash'jir...you know, the kind of elementals we fought against in Cataclysm. This seems like the problem of the World-Shaman.
Apparently, he's living in the Valley of Trials this whole time. Well, in that case, why isn't he off at the Maelstrom like he's supposed to be? Are his World-Shaman duties over? In that case, why isn't he off responding to Garrosh now? Some say it's because he wants to defend his family first, but that goes against everything we know about him as a selfless, charismatic leader.
Thrall's character is full of plot holes. And the only way to close those plot holes is by opening new ones.
4. The story can't progress with Thrall still around.
There's a reason he's called "Green Jesus." He's a messiah figure. He's always portrayed as selfless and being ultimately in the ethical right. Everything Thrall does is just and he's rarely ever called to question himself (as we saw in Elemental Bonds, which ultimately had no effect on his character).
WoW is supposed to be the story of us. That's why we're called heroes. We get vehicles like Tirion, Nazgrim and Taylor to be our voices, but ultimately, they are there to witness our deeds. They need us.
Thrall, however, doesn't need us. We are there to witness HIS deeds. We are there to be HIS henchmen. We are not allowed to steal HIS spotlight. It's always made clear that we need him to save us from our own stupidity.
And save us, Thrall shall. It's his role as a messiah to save us, as he saved the orcs. He is portrayed as redeeming us, as fixing the broken world, as being the unifying influence in the world. So long as he's around, he will forever rob us of agency as characters. Nothing we ever do will matter, none of the lives lost or the blood spilled will ever mean anything, because Thrall will always show up to save us at the end.
5. The story becomes stronger with Thrall dead.
Remove the messiah figure and you remove the certainty from the conflict and thus, make it more intense.
Think what happens if, say, Thrall is executed by Garrosh.
The Horde realizes that they have just killed the guy who always swore they weren't murderous monsters. Everything the Alliance and Cenarius has ever said about the Horde is suddenly proved true and Thrall isn't around anymore to save them. Suddenly, the Horde is left in a deep hole and the only way to get out is through their own will, their own deeds, their own grit. The story is theirs again. Not Thrall's.
And the Alliance realizes the last possibility of this ending at all peacefully has now been killed. The dream of living in peace with the Horde is over. From now on, it's kill or be killed. There is no easy way out anymore and there is no way they can sit back idly and wait for Thrall to fix it. Now, the Alliance must make its own peace.
Now see where we're at? No longer is it about bad versus good. We're now a real, authentic conflict. Two sides, both convinced they are in the right, hurtling toward each other at breakneck speeds. The Horde can't let themselves be ruled by this maniac, but they can't rely on the figures of the past to save them. The Alliance can't live with eternal war, but peace with the Horde is out of the question.
There's no more easy answers. Thus, we're invested to see what happens next.
Think it over.